The problem is that Nintendo did not just release one N64 emulator and leave it so people can download a ROM and a settings file. It seems they make a new emulator for each game, which is much more space consuming.

As of right now, our best hopes are to test ROMs in future released N64 games and see how they function.

I think there could still be another problem involved in all this! Another problem involved might be that when injecting a rom you not only use the blank emulator that comes with the rom but you also use texture patches etc. that are related to the original rom inside the wad! My guess is that some of these rom-specific contents of the rom might prevent some roms from working properly so to increase compatiblity a simple hex edit replacing the roms might not do but you would have to also change pointers to rom specific locations and make it all work more generally!